miaViz example data

Source: R/miaViz.R

These example data objects were prepared to serve as examples. See the details for more information.

data(col_graph)

data(row_graph)

data(row_graph_order)

Format

An object of class tbl_graph (inherits from igraph) of length 26.

An object of class tbl_graph (inherits from igraph) of length 996.

An object of class tbl_graph (inherits from igraph) of length 110.

Details

For *_graph data:

  1. “Jaccard” distances were calculated via calculateDistance(genus, FUN = vegan::vegdist, method = "jaccard", exprs_values = "relabundance"), either using transposed assay data or not to calculate distances for samples or features. NOTE: the function mia::calculateDistance is now deprecated.

  2. “Jaccard” dissimilarites were converted to similarities and values above a threshold were used to construct a graph via graph.adjacency(mode = "lower", weighted = TRUE).

  3. The igraph object was converted to tbl_graph via as_tbl_graph from the tidygraph package.